|
| Status |
Public on Jun 17, 2019 |
| Title |
Tabula Muris Senis (bulk RNA-seq) [I12_384Bulk_Plate2_S204] |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas_50
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57/BL6
tissue: Pancreas
age: 21 months postnatal
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT.
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv
|
| Data processing |
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned to the mm10plus genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv: Comma-separated text file includes gene count table for all organs and ages.
Supplementary_files_format_and_content: MACA_Bulk_metadata.csv: Comma-separated text file includes experiment metadata.
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Angela Oliveira Pisco |
| E-mail(s) |
angela.pisco@czbiohub.org
|
| Organization name |
CZ Biohub
|
| Department |
Data Sciences
|
| Street address |
499 Illinois St
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94103 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
|
| Relations |
| SRA |
SRX5900742 |
| BioSample |
SAMN11855046 |
